A TEM (Transmission Electron Microscope) and an STEM (Scanning Transmission Electron Microscope) are useful techniques for performing structural analysis and composition analysis at atomic levels of materials. However, the TEM acquires an image using an electron beam transmitted through a sample, and the structure in the acquired image reflects 2-dimensinoal symmetry. For this reason, there are demands to develop a method of acquiring a 3-dimensional tomogram using the TEM. Recently, development of a spherical aberration correcting apparatus enabled forming of an electromagnetic lens having a shallow DOF (Depth Of Field). Hence, by using the spherical aberration correcting apparatus and acquiring an image by varying a focal position, it is now possible to acquire the 3-dimensional tomogram. Actual observation examples using the spherical aberration correcting apparatus include pinpoint observation results of a boundary or a film deposited on a substrate surface reported in Japanese Laid-Open Patent Publication No. 2012-43563, and N. Shibata et al., “Atomic-scale imaging of individual dopant atoms in a buried interface”, Nature Materials, Vol. 8, August 2009, pp. 654-658, for example.
However, when acquiring the 3-dimensional tomogram using the TEM or the like, accurate positional relationship, and definite atomic deviation and distortion are required of the image that is acquired at each of a plurality of depth positions. For example, in the case of the sample in which a film made of a material having a composition different from that of a substrate is deposited on the substrate, it may be important to definitely know the relationship at the atomic level between the substrate and the film, and the atomic deviation and distortion of the film. However, according to a method proposed in Japanese Laid-Open Patent Publication No. 2012-43563, for example, the images at each of the substrate and the film are acquired by varying the focal position, and the sample moves (or drifts) at the atomic level while the focal position is varied. In a case in which the sample moves at the atomic level while the focal position is varied, it is difficult to detect the atomic deviation and distortion between the substrate and the film. In addition, because the film that is deposited on the substrate is thin, information of the substrate is included in the image of the film that is acquired, thereby making it difficult to detect the atomic deviation and distortion of the film deposited on the substrate.